Perform math operations on images
This task evaluates mathematical expressions involving existing
image files. The results of the calculations are stored in the
designated output file. Options are available to specify mathematical
expression directly or pre-defined expression for calculation of
spectral index image, and polarization intensity and position angle
images are available. The image file names imbedded in the expression or
specified in the imagename parameter for the pre-defined calculations may
be CASA images or FITS images.
NOTE: Index values start at 0 Use the imhead task to see the range of
index values for each axes.
Keyword arguments:
imagename input image name(s)
Default: none;
Examples: mode='evalexpr'; imagename=['image1.im', 'image2.im' ]
The text 'IM0' is replaced by 'image1.im' in the
expression and 'IM1' is repalced with 'image2.im'
mode='spix'; imagename=['image1.im','image2.im'] will calculate
an image of log(S1/S2)/log(f1/f2), where S1 and S2 are fluxes and
f1 and f2 are frequencies
mode='pola'; imagename='multistokes.im' (where that image contains both Q and U
stokes planes) or imagename=['imageQ.im','imageU.im'] will calculate
an image of polarization angle distribution, where imageQ.im and
imageU.im are Stokes Q and U images, respectively. Calculate 0.5*arctan(U/Q).
mode='poli'; imagename=['imageQ.im','imageU.im','imageV.im'] will calculate
total polarization intensity image, where imageQ.im, imageU.im, imageV.im
are Stokes Q, U, and V images, respectively. Alternatively, with
imagename = ['imageQ.im','imageU.im'] the linear polarization intensity
image will be calculated. In the case where imagename is a single multi-stokes
image, the total polarization image will be calculated if all of the Q, U, and
V stokes planes are present, and the linear polarization intensity image will
be calculated if the Q and U (but not V) planes are present.
mode mode for mathematical operation
Default: evalexpr
Options: 'evalexpr' : evalulate a mathematical expression defined in 'expr'
'spix' : spectalindex image
'pola' : polarization position angle image
'poli' : polarization intesity image
>>> mode expandable parameters
sigma (for mode='poli') standard deviation of noise of Stokes images with unit such as
Jy/beam to correct for bias
Default: '0.0Jy/beam' (= no debiasing)
polithresh (for mode='pola') Quantity (eg '30uJy/beam') describing the linear (not total;
the stokes V contribution is not included) polarization threshold. A mask ('mask0')
is written to the output image and is False for all corresponding linear polarization
values below this threshold. This parameter overrides the mask input parameter
(below). Default ('') means use the value given in mask, or no masking if that
value is empty as well.
expr (for mode='evalexpr') A LEL expression with images.
Image file names are specified in the imagenames paramter, and
the variables IM0, IM1, ... (or optionally via the varnames parameter, see below)
are used to represent these files
in the expression. Explicit notations of file names in the
expression are also supported, in which cases the file names must
be enclosed in double quotes (") and imagename is ignored.
Examples:
Make an image that is image1.im - image2.im
expr=' (IM0 - IM1 )'
or with an explicit notation,
expr='("image1.im" - "image2.im")'
Clip an image below a value (0.5 in this case)
expr = ' iif( IM0 >=0.5, IM0, 0.0) '
Note: iif (a, b, c) a is the boolean expression
b is the value if true
c is the value if false
Take the rms value of two images
expr = ' sqrt(IM0 * IM0 + IM1 * IM1) '
Note: No exponentiaion available?
Build an image pixel by pixel from the minimum of (image2.im, 2*image1.im)
expr='min(IM1,2*max(IM0))'
varnames For mode="evalexpr". Instead of the default variable names IM0, IM1, ..., use
the names in this array to represent the input images.
outfile The output image. Overwriting an existing outfile is not permitted.
Default: immath_results.im; Example: outfile='results.im'
mask Mask to use. See help par.mask. Default is none. Also see polithresh.
stretch Stretch the input mask if necessary and possible. See below.
region Name of region file, region text description, or region dictionary.
box A rectangular region on the directional plane expressed in pixels.
Example: box='10,10,50,50'
chans Channel ranges to use, expressed in pixels. Example: chans='3~20'
stokes Stokes parameters. Example: stokes='IQUV';
Options: 'I','Q','U','V','RR','RL','LR','LL','XX','YX','XY','YY', ...
Not used in for cases of mode='poli' or mode='pola'
Available functions in the expr and mask paramters:
pi(), e(), sin(), sinh(), asinh(), cos(), cosh(), tan(), tanh(),
atan(), exp(), log(), log10(), pow(), sqrt(), complex(), conj()
real(), imag(), abs(), arg(), phase(), aplitude(), min(), max()
round(), isgn(), floor(), ceil(), rebin(), spectralindex(), pa(),
iif(), indexin(), replace(), ...
If the mask has fewer dimensions than the image and if the shape
of the dimensions the mask and image have in common are the same,
the mask will automatically have the missing dimensions added so
it conforms to the image.
For a full description of the allowed syntax see the
Lattice Expression Language (LEL) documentation on the at:
http://aips2.nrao.edu/docs/notes/223/223.html
NOTE: where indexing and axis numbering are used in the above
functions they are 1-based, ie. numbering starts at 1.
If stretch is true and if the number of mask dimensions is less than
or equal to the number of image dimensions and some axes in the
mask are degenerate while the corresponding axes in the image are not,
the mask will be stetched in the degenerate axis dimensions. For example,
if the input image has shape [100, 200, 10] and the input
mask has shape [100, 200, 1] and stretch is true, the mask will be
stretched along the third dimension to shape [100, 200, 10]. However if
the mask is shape [100, 200, 2], stretching is not possible and an
error will result.
CAUTION: Note that when multiple image are used in the expression, there is
no garauntee about which of those images will be used to create the header
of the output image. Therefore, one may have to modify the output header as
needed if the input headers differ.
Examples:
# Double all values in an image.
immath( imagesname='myimage.im', expr='IM0*2', outfile='double.im' )
# or with an explicit notation,
immath( expr='"myimage.im"*2', outfile='double.im' )
# Taking the sin of an image and adding it to another
# Note that the images need to be the same size
immath(images=['image1.im', 'image2.im'], expr='sin(IM1)+IM0;',outfile='newImage.im')
# Adding only the plane associated with the 'V' stokes value and
# the 1st channel together in two images
immath(imagename=[image1', 'image2'], expr='IM0+IM1',chans='1',stokes='V')
# Selecting a single plane (5th channel), of the 3-D cube and
# adding it to the original image. In this example the 2-D plane
# gets expanded out and the values are applied to each plane in the
# 3-D cube.
default('immath')
imagename='ngc7538.image'
outfile='chanFive.im'
expr='IM0'
chans='5'
go
default('immath')
imagename=['ngc7538.image', chanFive.im']
outfile='ngc7538_chanFive.im'
expr='IM0+IM1'
go
# Selecting and saving the inner 3/4 of an image for channels 40,42,44
# as well as channels less than 10
default('immath')
imagename='my_image.im'
expr='IM0'
box='25,25,123,123'
chans='<10;40,42,44'
outfile='my_image_inner.im' )
go
# Dividing an image by another, making sure we aren't dividing by zero
default('immath')
imagename=['orion.image', 'my.image']
expr='IM0/iif(IM1==0,1.0,IM1)'
outfile='my_orion.image'
go
# Applying a mask to all of the images in the expression
default('immath')
imagename=['ngc7538.image','ngc7538_clean.image']
expr='(IM0*10)+IM1'
mask='"ngc7538.mask"'
outfile='really_noisy_ngc7538.image'
go
# Applying a pixel mask contained in the image information
default('immath')
imagename='ngc5921.image'
expr='IM0*10'
mask='mask("ngc5921.mask")'
outfile='ngc5921.masked.image'
go
# Creating a total polarization intensity image from an multi-stokes image
# containing IQUV.
default('immath')
outfile='pol_intensity'
stokes=''
# in imagename, you can also specify a list containing single stokes images
# of Q and U (for linear polarization intensity) and V (for total
# polarization intensity)
imagename='3C138_pcal'
mode='poli'
go
# Creating a polarization position angle image
default('immath')
outfile='pol_angle.im'
mode='pola'
# you can also do imagename=['Q.im','U.im'] for single stokes images, order of
# the two Stokes images does not matter
imagename='3C138_pcal' # multi-stokes image containing at least Q and U stokes
go
# same as before but write a mask with values of False for pixels for which the
# corresponding linear polarization ( sqrt(Q*Q+U*U)) is less than 30 microJy/beam
polithresh='30uJy/beam'
go
# Creating a spectral index image from the images at two different observing frequencies
default('immath')
outfile='mySource_sp.im'
mode='spix'
imagename=['mySource_5GHz.im','mySource_8GHz.im']
go
TEMPORARY IMAGES
At this time, it is usually necessary for this task to create intermediate, temporary disk images.
The names of these images start with '_immath' and are created in the directory in which the task
is run. The task makes reasonable attempts to remove these images before it exits, but there are
conceivably instances where the temporary images may not be automatically deleted. It is generally
safe to delete them by hand, assuming no immath instance is currently in progress.
The hope and plan is that the necessity of these images will decrease in the future (ie the computations
will require only RAM and not temporary persistent storage of intermediate results).
1.8.0